Proposed sporulation cascade for Clostridium difficile 630. Names of genes and proteins are derived from updated genome annotation (Additional file 2). Solid arrows in the putative regulatory cascade of C. difficile indicate confirmed interactions [15, 21], whereas dotted arrows indicate uncharacterized or postulated interactions. Operon structure or genomic region of (conserved) sporulation genes is given when relevant, and in vitro confirmed Spo0A binding sites are indicated with vertical blue bars. Genes are roughly aligned with the stage of sporulation at which they act, except for C. difficile sporulation genes that are not conserved in B. subtilis. When gene names start with spo, this has been omitted for clarity. CD3673 encodes a protein with high similarity to Spo0J. CD0125 encodes a protein with homology to B. subtilis spoIIQ. spoIV encodes a homolog of the B. subtilis YqfD protein. sigK is known as spoIIIC (N-terminal part) and spoIVCB (C-terminal part) in B. subtilis and is interrupted by a skin element. CD1231 encodes the recombinase in skin and is annotated as spoIVCA in B. subtilis. oxaA1 is known as spoIIIJ in B. subtilis. pth is known as spoVC in B. subtilis. spoVE is an FtsW-like protein and is sometimes annotated as such in C. difficile. The product of ftsH2 is the closest homolog of SpoVK of B. subtilis. C. difficile 630 encodes several SpoIIIE/FtsK like proteins. If and which one is associated with sporulation is unknown. cotF/cotCB and cotJB2/cotD are homologs of the B. subtilis genes cotJB and cotJC. SleB is also known as PrsW . CspBA is a serine protease. Proteins from this family in B. subtilis are not directly identified as sporulation specific. CspC is a germination receptor . sipL was hypothesized to encode a functional substitute for B. subtilis SpoVID . CD1613 (cotA), CD1511 (cotB), CD1433 (cotE), CD1567 (cotG) have been given a cot alias in a recent study . For the genes in grey the identification as homologs of the B. subtilis sporulation gene is tentative. Green colors indicate upregulated and red colors indicate downregulated in a spo0A mutant compared to the parental C. difficile 630∆erm strain at the transcriptome or proteome level in this study. Recently, the transcription of many genes - including most of the genes from this scheme - was identified as dependent on sporulation specific sigma factors [28, 29, 50].